Their victory ended an 18-year gap since the last French team reached the Uefa final - Bastia in 1978 - after striker Didier Tholot scored the 46th- minute winner.
The match failed to reach the heights of Bordeaux's stunning 3-0 quarter- final win over Milan, after they lost the first leg 2-0 in Italy, but the French club were rarely troubled by the Czechs on the way to their first European final.
The Bordeaux coach, Gernot Rohr, said: "It may not have been as thrilling as our match with Milan but it was more important because it has put us into the final. Now I believe we can win the trophy."
Dutch midfielder Richard Witschge said reaching the final was the end of a long road. "In all, we've beaten 11 teams to get this far. I would never have thought that possible," he said.
Despite a team boasting three exceptionally talented players in midfielder Zinedine Zidane, striker Christophe Dugarry and defender Bixente Lizarazu, all prime targets for foreign teams, including Arsenal, it can be no surprise the team have been unable to hit the heights on all fronts. League form has undoubtedly suffered though the club president, Alain Afflelou, will hear none of it.
"I know a lot of coaches were against entering the Intertoto Cup because they thought it would cut short players' holidays and damage pre-season preparations," he said.
"But I saw it as a reprieve for a team which had narrowly missed out on a Uefa Cup place. In the end, we only cut short holidays by three days and, instead of playing friendly matches, we were playing official games.
"Now I see lots of coaches from teams in mid-table are starting to talk about qualifying for the Intertoto Cup."
If Bordeaux have their name inscribed as 1996 Uefa Cup champions, it will all be considered worth it but, curiously, they will not go down as Inter toto winners.
The four teams who won their way into the Uefa Cup last summer were paired up in the preliminary round which also counted as the Intertoto semi-finals.
That left Bordeaux and another French team, Strasbourg, as Intertoto finalists, but it has apparently never been suggested that this final should ever be played.
Bayern, comprehensive quarter-final conquerors of Nottingham Forest, clinched a thrilling 4-3 aggregate win over Barcelona with a 2-1 victory at the Nou Camp.
The Spaniards were favourites to reach the final after holding Bayern to a 2-2 draw in Germany but Mehmet Scholl set up Bayern for the vital opening goal.
Wing back Markus Babbel, whose terrible back-pass in the first leg led to Barcelona's second goal, made amends by putting Bayern ahead in the 40th minute and the Germans went clear seven minutes from time when Marcel Witezcek made it 2-0.
Substitute Ivan de la Pena scored a consolation goal for Barcelona two minutes from time as his side tried desperately to force extra time.
The arrival of De la Pena in the final minutes changed the game in which Barcelona had badly missed the Romanian playmaker Gheorghe Hagi, who was out with injury.
Without a natural set-piece specialist, the Barcelona coach, Johan Cruyff, turned to Hagi's compatriot Gheorghe Popescu to take a series of dangerous free-kicks that the Spaniards forced in the opening 15 minutes.
But neither Popescu nor the Bosnian striker Meho Kodro, who was twice guilty of wasting passes after being put through by Jordi Cruyff, could make the best of Barcelona's early dominance.
Bayern's victory, which followed last week's Spanish Cup final extra- time defeat against Atletico Madrid and a disappointing draw against Racing Santander over the weekend to lose ground in the title race, also ended Barcelona's unbeaten home record this season to complete their miserable week.
But Cruyff remained philosophical, claiming: "We have to be happy - you have to play well to be still playing the competitions at the end of the season."Reuse content